Theoretical insights into the nature of halogen bonding in prereactive complexes.
Ontology highlight
ABSTRACT:
SUBMITTER: Hill JG
PROVIDER: S-EPMC3790957 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In this manuscript, we combined ab initio calculations (RI-MP2/def2-TZVPD level of theory) and a search in the CSD (Cambridge Structural Database) to analyze the influence of aromatic substitution in charge-assisted multivalent halogen bonding complexes. We used a series of benzene substituted iodine derivatives C₆H₄(IF₄)Y (Y = H, NH₂, OCH₃, F, CN, and CF₃) as Lewis acids and used Cl- as electron rich interacting atoms. We have represented the Hammett's plot and observed a good regression coefficient (interaction energies vs. Hammett's σ parameter). Additionally, we demonstrated the direct correlation between the Hammett's σ parameter and the value of molecular electrostatic potential measured at the I atom on the extension of the C-I bond. Furthermore, we have carried out AIM (atoms in molecules) and NBO (natural bonding orbital) analyses to further describe and characterize the interactions described herein. Finally, we have carried out a search in the CSD (Cambridge Structural Database) and found several X-ray structures where these interactions are present, thus giving reliability to the results derived from the calculations.
| S-EPMC5943962 | biostudies-literature
Project description:The strong, specific, and directional halogen bond (XB) is an ideal supramolecular synthon in crystal engineering, as well as rational catalyst and drug design. These attributes attracted strong growing interest in halogen bonding in the past decade and led to a wide range of applications in materials, biological, and catalysis applications. Recently, various research groups exploited the XB mode of activation in designing halogen-based Lewis acids in effecting organic transformation, and there is continual growth in this promising area. In addition to the rapid advancements in methodology development, computational investigations are well suited for mechanistic understanding, rational XB catalyst design, and the study of intermediates that are unstable when observed experimentally. In this review, we highlight recent computational studies of XB organocatalytic reactions, which provide valuable insights into the XB mode of activation, competing reaction pathways, effects of solvent and counterions, and design of novel XB catalysts.
| S-EPMC7179134 | biostudies-literature
Project description:We employ a variety of natural bond orbital (NBO) and natural resonance theory (NRT) tools to comprehensively investigate the nature of halogen and pnicogen bonding interactions in RPH2···IF/FI binary complexes (R = CH3, OH, CF3, CN, and NO2) and the tuning effects of R-substituents. Though such interactions are commonly attributed to "sigma-hole"-type electrostatic effects, we show that they exhibit profound similarities and analogies to the resonance-type 3-center, 4-electron (3c/4e) donor-acceptor interactions of hydrogen bonding, where classical-type "electrostatics" are known to play only a secondary modulating role. The general 3c/4e resonance perspective corresponds to a continuous range of interatomic A···B bond orders (bAB), spanning both the stronger "covalent" interactions of the molecular domain (say, bAB ≥ ½) and the weaker interactions (bAB ˂ ½, often misleadingly termed "noncovalent") that underlie supramolecular complexation phenomena. We show how a unified NBO/NRT-based description of hydrogen, halogen, pnicogen, and related bonding yields an improved predictive utility and intuitive understanding of empirical trends in binding energies, structural geometry, and other measurable properties that are expected to be manifested in all such supramolecular interaction phenomena.
| S-EPMC6600247 | biostudies-literature
Project description:As an important intermolecular interaction, halogen bonding has been studied extensively, but its nature still suffers from controversy without one uniform essence. Electrostatics, charge transfer, polarization and dispersion are emphasized, but the covalent nature is usually overlooked except for the strong halogen bonding species I3 -, which is widely accepted as a result of a three-center four-electron (3c-4e) interaction. In our study, the potential energy surface of I3 - has been evaluated to explore the dissociation from I3 - to I2⋯I-. We found that different from an equivalent 3c-4e bond in I3 -, I2⋯I- can be rationalized by a polarized one. In addition, when the orbitals are polarized, it is exactly what traditional charge transfer or the popular σ-hole picture describes. I3 - can be described by the Lewis theory model with the middle I+ cation serving as the Lewis acid and two terminal I- anions acting as Lewis base. Therefore, we further extended this model to a series of I-containing species with chemical composition of L-I+-L, F--I+-L and H3P-I+-L (L = OH-, F-, Cl-, Br-, I-, PH3, NH3, H2S, HI, H2O, HBr and HCl) to explore the nature of halogen bonding. When the forces of two bases around I+ are the same, it corresponds to an equivalent 3c-4e bond, such as I3 -. Otherwise, it is a polarized multicenter bond, such as I2⋯I-. This work gives a new insight into the nature of halogen bonding compounds: besides the well-known I3 -, the nature of the other species is also a multicenter bond, existing as equivalent and polarized 3c-4e bonds, respectively.
| S-EPMC9042191 | biostudies-literature
Project description:The LIM-domain kinase (LIMK) family consists of two isoforms, LIMK1 and LIMK2, which are highly homologous, making selective inhibitor development challenging. LIMK regulates dynamics of the actin cytoskeleton, thereby impacting many cellular functions including cell morphology and motility. Here, we designed and synthesised analogues of a known pyrrolopyrimidine LIMK inhibitor with moderate selectivity for LIMK1 over LIMK2 to gain insights into which features contribute to both activity and selectivity. We incorporated a different stereochemistry around a cyclohexyl central moiety to achieve better selectivity for different LIMK isoforms. Inhibitory activity was assessed by kinase assays, and biological effects in cells were determined using an in vitro wound closure assay. Interestingly, a slight change in stereochemistry alters LIMK isoform selectivity. Finally, a docking study was performed to predict how the new compounds interact with the target.
| S-EPMC8711653 | biostudies-literature
Project description:The concept of the halogen bond (or X-bond) has become recognized as contributing significantly to the specificity in recognition of a large class of halogenated compounds. The interaction is most easily understood as primarily an electrostatically driven molecular interaction, where an electropositive crown, or σ-hole, serves as a Lewis acid to attract a variety of electron-rich Lewis bases, in analogous fashion to a classic hydrogen bonding (H-bond) interaction. We present here a broad overview of X-bonds from the perspective of a biologist who may not be familiar with this recently rediscovered class of interactions and, consequently, may be interested in how they can be applied as a highly directional and specific component of the molecular toolbox. This overview includes a discussion for where X-bonds are found in biomolecular structures, and how their structure-energy relationships are studied experimentally and modeled computationally. In total, our understanding of these basic concepts will allow X-bonds to be incorporated into strategies for the rational design of new halogenated inhibitors against biomolecular targets or toward molecular engineering of new biological-based materials.
| S-EPMC3588911 | biostudies-literature
Project description:Halogen bonding is often described as being driven predominantly by electrostatics, and thus adducts between anionic halogen bond (XB) donors (halogen-based Lewis acids) and anions seem counterintuitive. Such "anti-electrostatic" XBs have been predicted theoretically but for organic XB donors, there are currently no experimental examples except for a few cases of self-association. Reported herein is the synthesis of two negatively charged organoiodine derivatives that form anti-electrostatic XBs with anions. Even though the electrostatic potential is universally negative across the surface of both compounds, DFT calculations indicate kinetic stabilization of their halide complexes in the gas phase and particularly in solution. Experimentally, self-association of the anionic XB donors was observed in solid-state structures, resulting in dimers, trimers, and infinite chains. In addition, co-crystals with halides were obtained, representing the first cases of halogen bonding between an organic anionic XB donor and a different anion. The bond lengths of all observed interactions are 14-21?% shorter than the sum of the van der Waals radii.
| S-EPMC7317790 | biostudies-literature
Project description:Homogeneous catalysis by gold involves organogold complexes as precatalysts and reaction intermediates. Fundamental knowledge of the gold-carbon bonding is critical to understanding the catalytic mechanisms. However, limited spectroscopic information is available about organogolds that are relevant to gold catalysts. Here we report an investigation of the gold-carbon bonding in gold(I)-alkynyl complexes using photoelectron spectroscopy and theoretical calculations. We find that the gold-carbon bond in the ClAu-CCH(-) complex represents one of the strongest gold-ligand bonds-even stronger than the known gold-carbon multiple bonds, revealing an inverse correlation between bond strength and bond order. The gold-carbon bond in LAuCCH(-) is found to depend on the ancillary ligands and becomes stronger for more electronegative ligands. The strong gold-carbon bond underlies the catalytic aptness of gold complexes for the facile formation of terminal alkynyl-gold intermediates and activation of the carbon-carbon triple bond.
| S-EPMC5882230 | biostudies-literature
Project description:In recent years, the non-covalent interaction of halogen bonding (XB) has found increasing application in organocatalysis. However, reports of the activation of metal-ligand bonds by XB have so far been limited to a few reactions with elemental iodine or bromine. Herein, we present the activation of metal-halogen bonds by two classes of inert halogen bond donors and the use of the resulting activated complexes in homogenous gold catalysis. The only recently explored class of iodolium derivatives were shown to be effective activators in two test reactions and their activity could be modulated by blocking of the Lewis acidic sites. Bis(benzimidazolium)-based halogen bonding activators provided even more rapid conversion, while the non-iodinated reference compound showed little activity. The role of halogen bonding in the activation of metal-halogen bonds was further investigated by NMR experiments and DFT calculations, which support the mode of activation occurring via halogen bonding.
| S-EPMC7540446 | biostudies-literature
Project description:We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX???A(-) and the analogous hydrogen-bonded complexes DH???A(-) (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn-Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX???A(-) arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO-LUMO interactions between the lone pair of A(-) and the ?* orbital of D-X.
| S-EPMC3922460 | biostudies-literature